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Coexpression cluster:C964: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004535!3.60e-13!110;UBERON:0000475!3.60e-13!365;UBERON:0001009!1.62e-12!113;UBERON:0000490!2.08e-12!138;UBERON:0002049!5.64e-12!79;UBERON:0007798!5.64e-12!79;UBERON:0000914!8.21e-12!83;UBERON:0002329!8.21e-12!83;UBERON:0003077!8.21e-12!83;UBERON:0003059!8.21e-12!83;UBERON:0007282!8.21e-12!83;UBERON:0009618!8.21e-12!83;UBERON:0007285!8.21e-12!83;UBERON:0000481!4.78e-11!347;UBERON:0004290!1.04e-10!70;UBERON:0001134!1.30e-10!61;UBERON:0002036!1.30e-10!61;UBERON:0003082!1.30e-10!61;UBERON:0002385!2.23e-10!63;UBERON:0001015!2.23e-10!63;UBERON:0000383!2.23e-10!63;UBERON:0000477!4.20e-10!286;UBERON:0004872!6.32e-10!84;UBERON:0001981!8.18e-10!60;UBERON:0007500!8.18e-10!60;UBERON:0004537!8.18e-10!60;UBERON:0006965!8.18e-10!60;UBERON:0000055!1.11e-09!69;UBERON:0002100!2.83e-09!216;UBERON:0005256!3.97e-09!143;UBERON:0000119!2.68e-08!312;UBERON:0001637!2.86e-08!42;UBERON:0003509!2.86e-08!42;UBERON:0004572!2.86e-08!42;UBERON:0000486!3.45e-08!82;UBERON:0004573!3.78e-08!33;UBERON:0004571!3.78e-08!33;UBERON:0003914!4.11e-08!118;UBERON:0000483!4.31e-08!309;UBERON:0003104!2.93e-07!238;UBERON:0009142!2.93e-07!238;UBERON:0004111!4.06e-07!241
|ontology_enrichment_uberon=UBERON:0004535!3.60e-13!110;UBERON:0000475!3.60e-13!365;UBERON:0001009!1.62e-12!113;UBERON:0000490!2.08e-12!138;UBERON:0002049!5.64e-12!79;UBERON:0007798!5.64e-12!79;UBERON:0000914!8.21e-12!83;UBERON:0002329!8.21e-12!83;UBERON:0003077!8.21e-12!83;UBERON:0003059!8.21e-12!83;UBERON:0007282!8.21e-12!83;UBERON:0009618!8.21e-12!83;UBERON:0007285!8.21e-12!83;UBERON:0000481!4.78e-11!347;UBERON:0004290!1.04e-10!70;UBERON:0001134!1.30e-10!61;UBERON:0002036!1.30e-10!61;UBERON:0003082!1.30e-10!61;UBERON:0002385!2.23e-10!63;UBERON:0001015!2.23e-10!63;UBERON:0000383!2.23e-10!63;UBERON:0000477!4.20e-10!286;UBERON:0004872!6.32e-10!84;UBERON:0001981!8.18e-10!60;UBERON:0007500!8.18e-10!60;UBERON:0004537!8.18e-10!60;UBERON:0006965!8.18e-10!60;UBERON:0000055!1.11e-09!69;UBERON:0002100!2.83e-09!216;UBERON:0005256!3.97e-09!143;UBERON:0000119!2.68e-08!312;UBERON:0001637!2.86e-08!42;UBERON:0003509!2.86e-08!42;UBERON:0004572!2.86e-08!42;UBERON:0000486!3.45e-08!82;UBERON:0004573!3.78e-08!33;UBERON:0004571!3.78e-08!33;UBERON:0003914!4.11e-08!118;UBERON:0000483!4.31e-08!309;UBERON:0003104!2.93e-07!238;UBERON:0009142!2.93e-07!238;UBERON:0004111!4.06e-07!241
|tf_chipseq_enrich=CEBPB#1051;5:4.42841534768045:0.0025225868523706:0.0139883427989133!EGR1#1958;8:4.43393697316457:1.92853122912633e-05:0.000435489455218865!ELK4#2005;7:12.6277524010307:1.08190108922051e-07:6.31243954508943e-06!ETS1#2113;4:4.32389374320104:0.00918753673932392:0.0347482128455947!FOXA1#3169;5:6.15634430521414:0.00055192590587499:0.00471282721639098!FOXA2#3170;5:13.6835909737029:1.21001374207767e-05:0.000302979202131022!HEY1#23462;8:3.59120981609396:9.88548321897326e-05:0.00139254111398213!IRF1#3659;5:4.24286875197995:0.00306203286774801:0.0161464026393383!MXI1#4601;4:4.42736516833747:0.00844465741513493:0.032780210956301!POLR2A#5430;9:2.14745317655807:0.00102941289260802:0.00729035417990706!SRF#6722;5:7.66509903453767:0.000196444781216345:0.00236174703642844!TAF1#6872;8:2.97159669844026:0.000423374995123481:0.00395995532112675!USF1#7391;5:3.53416626511553:0.0069229675408181:0.02931154201952!USF2#7392;6:8.66146492337973:1.42236000274901e-05:0.000340398387550651
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}}
}}

Revision as of 14:11, 5 September 2012


Full id: C964_Nucleus_Anulus_meningioma_large_Olfactory_Chondrocyte_Mesothelial



Phase1 CAGE Peaks

Hg19::chrX:119694291..119694298,-p21@CUL4B
Hg19::chrX:119694334..119694362,-p5@CUL4B
Hg19::chrX:119694463..119694476,-p17@CUL4B
Hg19::chrX:119694505..119694522,-p8@CUL4B
Hg19::chrX:119694538..119694549,-p20@CUL4B
Hg19::chrX:119694573..119694611,-p2@CUL4B
Hg19::chrX:119694622..119694642,-p3@CUL4B
Hg19::chrX:119694719..119694730,-p14@CUL4B
Hg19::chrX:119694739..119694751,-p12@CUL4B


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
cardiovascular system3.60e-13110
organism subdivision3.60e-13365
circulatory system1.62e-12113
unilaminar epithelium2.08e-12138
vasculature5.64e-1279
vascular system5.64e-1279
somite8.21e-1283
paraxial mesoderm8.21e-1283
presomitic mesoderm8.21e-1283
presumptive segmental plate8.21e-1283
trunk paraxial mesoderm8.21e-1283
presumptive paraxial mesoderm8.21e-1283
multi-tissue structure4.78e-11347
dermomyotome1.04e-1070
skeletal muscle tissue1.30e-1061
striated muscle tissue1.30e-1061
myotome1.30e-1061
muscle tissue2.23e-1063
musculature2.23e-1063
musculature of body2.23e-1063
anatomical cluster4.20e-10286
splanchnic layer of lateral plate mesoderm6.32e-1084
blood vessel8.18e-1060
epithelial tube open at both ends8.18e-1060
blood vasculature8.18e-1060
vascular cord8.18e-1060
vessel1.11e-0969
trunk2.83e-09216
trunk mesenchyme3.97e-09143
cell layer2.68e-08312
artery2.86e-0842
arterial blood vessel2.86e-0842
arterial system2.86e-0842
multilaminar epithelium3.45e-0882
systemic artery3.78e-0833
systemic arterial system3.78e-0833
epithelial tube4.11e-08118
epithelium4.31e-08309
mesenchyme2.93e-07238
entire embryonic mesenchyme2.93e-07238
anatomical conduit4.06e-07241


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105154.428415347680450.00252258685237060.0139883427989133
EGR1#195884.433936973164571.92853122912633e-050.000435489455218865
ELK4#2005712.62775240103071.08190108922051e-076.31243954508943e-06
ETS1#211344.323893743201040.009187536739323920.0347482128455947
FOXA1#316956.156344305214140.000551925905874990.00471282721639098
FOXA2#3170513.68359097370291.21001374207767e-050.000302979202131022
HEY1#2346283.591209816093969.88548321897326e-050.00139254111398213
IRF1#365954.242868751979950.003062032867748010.0161464026393383
MXI1#460144.427365168337470.008444657415134930.032780210956301
POLR2A#543092.147453176558070.001029412892608020.00729035417990706
SRF#672257.665099034537670.0001964447812163450.00236174703642844
TAF1#687282.971596698440260.0004233749951234810.00395995532112675
USF1#739153.534166265115530.00692296754081810.02931154201952
USF2#739268.661464923379731.42236000274901e-050.000340398387550651



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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